Experiment 4
Full experimental information, including previous experiments and timeline, can be found at the MCP website
library(phyloseq)
library(reshape2)
library(tidyverse)
library(vegan)
library(HTSSIP)
library(ape)
library(CoDaSeq)
library(philr)
library(ggtree)
library(cowplot)
library(ggplot2)
library(viridis)
library(phytools)State Data
Gas Data
Full gas data for the entire experiment can be found at the Experiment 4 highcharts website
x<-read.csv(file='/Users/oliviaahern/Documents/R/Exp4/22Apr22/Exp4_Chemostat.csv',header=TRUE)
timec=x$Time..d.
mc1cO2c=x$CO2.MC1....
mc2cO2c=x$CO2.MC2....
mc3cO2c=x$CO2.MC3....
mc4cO2c=x$CO2.MC4....
mc5cO2c=x$CO2.MC5....
mc6cO2c=x$CO2.MC6....
mc1O2c=x$O2.MC1....
mc2O2c=x$O2.MC2....
mc3O2c=x$O2.MC3....
mc4O2c=x$O2.MC4....
mc5O2c=x$O2.MC5....
mc6O2c=x$O2.MC6....
x<-read.csv(file='/Users/oliviaahern/Documents/R/Exp4/22Apr22/Exp4_Batch.csv',header=TRUE)
time=x$Time..d.
mc1cO2=x$CO2.MC1....
mc2cO2=x$CO2.MC2....
mc3cO2=x$CO2.MC3....
mc4cO2=x$CO2.MC4....
mc5cO2=x$CO2.MC5....
mc6cO2=x$CO2.MC6....
mc1O2=x$O2.MC1....
mc2O2=x$O2.MC2....
mc3O2=x$O2.MC3....
mc4O2=x$O2.MC4....
mc5O2=x$O2.MC5....
mc6O2=x$O2.MC6....
par(mfrow=c(2,2),mar=c(5,5,1,1))
layout(matrix(c(1,2,2,3,4,4), nrow = 2, ncol = 3, byrow = TRUE))
plot(time,mc1O2, type='l',pch=21, col='gray70',ylim=c(20.8,21.2),
xlab="Time (days)", lwd=1, cex.axis=1.5,cex.lab = 1.5,
ylab="Oxygen (%)", yaxt='n')
axis(2, at=c(20.8, 21, 21.2), cex.axis=1.5)
lines(time, mc2O2, type='l', pch=21, col='#a44f9a')
lines(time, mc3O2, type='l', pch=21, col='#6870c8')
lines(time, mc4O2, type='l', pch=21, col='#56ae6c')
lines(time, mc5O2, type='l', pch=21, col='#af953c')
lines(time, mc6O2, type='l', pch=21, col='#ba4a4f')
plot(timec,mc1O2c, type='l',pch=21, col='gray70',ylim=c(20.5,21),
xlab="Time (days)", lwd=1,cex.axis=1.5,cex.lab = 1.5,
ylab="Oxygen (%)", yaxt="n")
axis(2, at=c(20.6, 20.8,21), cex.axis=1.5)
lines(timec, mc2O2c, type='l', pch=21, col='#a44f9a')
lines(timec, mc3O2c, type='l', pch=21, col='#6870c8')
lines(timec, mc4O2c, type='l', pch=21, col='#56ae6c')
lines(timec, mc5O2c, type='l', pch=21, col='#af953c')
lines(timec, mc6O2c, type='l', pch=21, col='#ba4a4f')
plot(time,mc1cO2, type='l',pch=21, col='gray70',ylim=c(0,0.2),
xlab="Time (days)", lwd=1,cex.axis=1.5,cex.lab = 1.5,
ylab="Carbon Dioxide (%)", yaxt='n')
axis(2, at=c(0,0.1,0.2), cex.axis=1.5)
lines(time, mc2cO2, type='l', pch=21, col='#a44f9a')
lines(time, mc3cO2, type='l', pch=21, col='#6870c8')
lines(time, mc4cO2, type='l', pch=21, col='#56ae6c')
lines(time, mc5cO2, type='l', pch=21, col='#af953c')
lines(time, mc6cO2, type='l', pch=21, col='#ba4a4f')
plot(timec,mc1cO2c, type='l',pch=21, col='gray70',ylim=c(0.18,0.3),
xlab="Time (days)", lwd=1,cex.axis=1.5,cex.lab = 1.5,
ylab="Carbon Dioxide (%)", yaxt="n")
axis(2, at=c(0.2, 0.25,0.3), cex.axis=1.5)
lines(timec, mc2cO2c, type='l', pch=21, col='#a44f9a')
lines(timec, mc3cO2c, type='l', pch=21, col='#6870c8')
lines(timec, mc4cO2c, type='l', pch=21, col='#56ae6c')
lines(timec, mc5cO2c, type='l', pch=21, col='#af953c')
lines(timec, mc6cO2c, type='l', pch=21, col='#ba4a4f')
Atomic % 13C
Atomic % 13C was measured from dried GFF filters. Calculations and measurements were carried out by the MBL Stable Isotope
read=read.csv(file="/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/SIP_Spins/atomic_C_30Aug22.csv",header=T)
read1=subset(read, B_C=="B")
MC1=subset(read1, MC=="MC1")
MC2=subset(read1, MC=="MC2")
MC3=subset(read1, MC=="MC3")
MC4=subset(read1, MC=="MC4")
MC5=subset(read1,MC=="MC5")
MC6=subset(read1,MC=="MC6")
read2=subset(read, B_C=="C")
MC1c=subset(read2, MC=="MC1")
MC2c=subset(read2, MC=="MC2")
MC3c=subset(read2, MC=="MC3")
MC4c=subset(read2, MC=="MC4")
MC5c=subset(read2,MC=="MC5")
MC6c=subset(read2,MC=="MC6")
{par(mar=c(5,5,1,1), mfrow=c(1,2))
plot(MC1$TP,MC1$mm_atomic_C, type='o', ylim=c(0,10542.03827),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.5, cex.lab=1.4)
lines(MC1$TP, MC2$mm_atomic_C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.5)
lines(MC1$TP, MC3$mm_atomic_C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.5)
lines(MC1$TP, MC4$mm_atomic_C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.5)
lines(MC1$TP, MC5$mm_atomic_C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.5)
lines(MC1$TP, MC6$mm_atomic_C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.5)
legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
"MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
plot(MC1c$TP,MC1c$mm_atomic_C, type='o', ylim=c(0,13424.45736),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.5, cex.lab=1.4)
lines(MC1c$TP, MC2c$mm_atomic_C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.5)
lines(MC1c$TP, MC3c$mm_atomic_C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.5)
lines(MC1c$TP, MC4c$mm_atomic_C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.5)
lines(MC1c$TP, MC5c$mm_atomic_C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.5)
lines(MC1c$TP, MC6c$mm_atomic_C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.5)
legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
"MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
}
Atomic % 13C + POC
Atomic % 13C was measured from dried GFF filters. Calculations and measurements were carried out by the MBL Stable Isotope. POC was normalized to the amount of water filtered through each sample.
{#par(mar=c(5,5,1,1), mfrow=c(2,2))
layout(matrix(c(1,2,2,3,4,4), nrow = 2, ncol = 3, byrow = TRUE))
plot(MC1$TP,MC1$Balanced_Atomic_.13C, type='o', ylim=c(0,30),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,10,20,30))
lines(MC1$TP, MC2$Balanced_Atomic_.13C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1$TP, MC3$Balanced_Atomic_.13C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1$TP, MC4$Balanced_Atomic_.13C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1$TP, MC5$Balanced_Atomic_.13C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1$TP, MC6$Balanced_Atomic_.13C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
# legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
# "MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
# pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
plot(MC1c$TP,MC1c$Balanced_Atomic_.13C, type='o', ylim=c(0,30),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,10,20,30))
lines(MC1c$TP, MC2c$Balanced_Atomic_.13C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1c$TP, MC3c$Balanced_Atomic_.13C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1c$TP, MC4c$Balanced_Atomic_.13C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1c$TP, MC5c$Balanced_Atomic_.13C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1c$TP, MC6c$Balanced_Atomic_.13C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
#legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
# "MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
# pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
plot(MC1$TP,MC1$POC.._M., type='o', ylim=c(0,500),pch=21,bg='gray70',
xlab="Time (days)", ylab="POC (uM)", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,250,500))
lines(MC1$TP, MC2$POC.._M., type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1$TP, MC3$POC.._M., type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1$TP, MC4$POC.._M., type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1$TP, MC5$POC.._M., type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1$TP, MC6$POC.._M., type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
plot(MC1c$TP,MC1c$POC.._M., type='o', ylim=c(0,1100),pch=21,bg='gray70',
xlab="Time (days)", ylab="POC (uM)", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,500,1000))
lines(MC1c$TP, MC2c$POC.._M., type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1c$TP, MC3c$POC.._M., type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1c$TP, MC4c$POC.._M., type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1c$TP, MC5c$POC.._M., type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1c$TP, MC6c$POC.._M., type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
}
SIP Spins
SIP gradients were setup using a CsTFA gradient centered at ~1.80 g/mL, formamide, and between 750-500 ng of RNA. Samples were spun using an ultracentrifuge spinning at 65,000 rpm at 20C for 65 hours.
Correction factors include Lueder’s Buoyant density (Lueders et al, 2010) and the Buckley Lab RNA SIP protocol.
Standard deviation between SIP runs (as of Sept 9th, 2022) were:
- Lueders BD and correction factor: 0.004110266 +/- 0.001662171 g/mL (~40% standard deviation)
- Buckley BD and correction factor: 0.00309178 +/- 0.001010027 g/mL (~33% standard deviation)
C13 peak was about 0.016 g/mL higher than the 13C peak.
Batch
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
dim(read)## [1] 343 14Ribogreen Raw
MC1-C12
MC1_T2.5=subset(read, read$MC=="MC1" & TP =="2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP =="3.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP =="4.5")
## Colors
# MC1 - gray 70
# MC2 #a44f9a
# MC3 #6870c8
# MC4 #56ae6c
# MC5 #af953c
# MC6 #ba4a4f
# C12-T2.5 and 3.5
par(mfrow=c(1,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.75))
lines(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
MC1-C12 vs. MC2-Met
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.2))
lines(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,4.6))
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#a44f9a")
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
plot(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#a44f9a")
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_conc,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
}
MC1-C12 vs. MC3-Eth
# MC1-T2.5 and MC3-Eth-T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_conc,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.2))
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#6870c8")
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
plot(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#6870c8")
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_conc,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
}
MC1-C12 vs. MC4-Ace
######
# MC1 - T2.5 vs. MC4 - Ace
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_conc,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,0.7))
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#56ae6c")
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
plot(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#56ae6c")
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_conc,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
}
MC1-C12 vs. MC5-Glu
# MC1 vs MC5
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_conc,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1))
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#af953c")
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_RMAX,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
plot(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#af953c")
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_conc,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
}
MC1-C12 vs. MC6-Xyl
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_RMAX,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_conc,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.5))
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#ba4a4f")
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_RMAX,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#ba4a4f")
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_conc,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
}
Ribo - Buckley
MC1- C12
par(mfrow=c(1,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.75))
lines(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
#### MC1-C12- vs. MC2-Met
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.2))
lines(MC2_T2.5$Buckley, MC2_T2.5$Ribo_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,4.6))
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#a44f9a")
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
plot(MC2_T2.5$Buckley, MC2_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#a44f9a")
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_conc,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
}
MC1-C12 vs. MC3-Eth
# MC1-T2.5 and MC3-Eth-T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC3_T2.5$Buckley, MC3_T2.5$Ribo_conc,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.2))
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#6870c8")
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
plot(MC3_T2.5$Buckley, MC3_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#6870c8")
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_conc,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
}
MC1-C12 vs. MC4-Ace
######
# MC1 - T2.5 vs. MC4 - Ace
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC4_T2.5$Buckley, MC4_T2.5$Ribo_conc,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,0.7))
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#56ae6c")
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
plot(MC4_T2.5$Buckley, MC4_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#56ae6c")
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_conc,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
}
MC1-C12 vs. MC5-Glu
# MC1 vs MC5
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC5_T2.5$Buckley, MC5_T2.5$Ribo_conc,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1))
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#af953c")
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_RMAX,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
plot(MC5_T2.5$Buckley, MC5_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#af953c")
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_conc,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
}
MC1-C12 vs. MC6-Xyl
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC6_T2.5$Buckley, MC6_T2.5$Ribo_conc,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.5))
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#ba4a4f")
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_RMAX,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Buckley, MC6_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#ba4a4f")
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_conc,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
}
Ribo Correct Both
MC1-C12 vs. MC2-Met
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc. (ribogreen)", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Corrected, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T3.5$Corrected, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc. ", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T4.5$Corrected, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC2_T2.5$Corrected, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.735,1.85),
col="#a44f9a")
lines(MC2_T3.5$Corrected, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Corrected, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5", "MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a","#a44f9a"), bty='n')
plot(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.735,1.85),
col="#a44f9a")
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5", "MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a","#a44f9a"), bty='n')
}
MC1-C12 vs. MC3-Eth
# MC1-T2.5 and MC3-Eth-T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Corrected, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T3.5$Corrected, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T4.5$Corrected, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC3_T2.5$Corrected, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#6870c8',pch=21, xlim=c(1.735,1.85),
col="#6870c8")
lines(MC3_T3.5$Corrected, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Corrected, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5", "MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8","#6870c8"), bty='n')
plot(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc. ", bg='#6870c8',pch=21, xlim=c(1.735,1.85),
col="#6870c8")
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5", "MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8","#6870c8"), bty='n')
}
MC1-C12 vs. MC4-Ace
######
# MC1 - T2.5 vs. MC4 - Ace
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T2.5$Corrected, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T3.5$Corrected, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T4.5$Corrected, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC4_T2.5$Corrected, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.74,1.84),
col="#56ae6c")
lines(MC4_T3.5$Corrected, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Corrected, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5", "MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c","#56ae6c"), bty='n')
plot(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.74,1.84),
col="#56ae6c")
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5", "MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c","#56ae6c"), bty='n')
}
MC1-C12 vs. MC5-Glu
# MC1 vs MC5
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(3,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T2.5$Corrected, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T3.5$Corrected, MC5_T3.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC5_T2.5$Corrected, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.7, 1.83),
col="#af953c")
lines(MC5_T3.5$Corrected, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("#af953c", "#af953c"), bty='n', cex=0.9)
plot(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.7, 1.83),
col="#af953c")
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("#af953c", "#af953c"), bty='n', cex=0.9)
}
MC1-C12 vs. MC6-Xyl
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(3,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC6_T2.5$Corrected, MC6_T2.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.84))
lines(MC6_T3.5$Corrected, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.75, 1.85))
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC6_T2.5$Corrected, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.7, 1.84),
col="#ba4a4f")
lines(MC6_T3.5$Corrected, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n', cex=0.9)
plot(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.75, 1.85),
col="#ba4a4f")
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n', cex=0.9)
}
Fig for talk
{
par(mar=c(5,5,1,1))
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density (g/mL)",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.84), ylim=c(0,1),
yaxt='n',xaxt='n', cex.lab=1.2, bty='n',cex=1.4)
rect(xleft=1.787, xright=1.794, ybottom=0, ytop=1.03, col= rgb(0.9960784,0.9411765,0.2745098,alpha=0.8),lty=1, lwd=0)
#rect(xleft=1.807990115-0.0035, xright=1.807990115+0.0035, ybottom=0, ytop=1.03, col= rgb(0.5529412,0.08627451,0.08627451,alpha=0.7),lty=1, lwd=0)
rect(xleft=1.807990115-0.0035, xright=1.807990115+0.0035, ybottom=0, ytop=1.03, col= rgb(0.9058824,0.1803922,0.1803922,alpha=0.3),lty=1, lwd=0)
lines(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", pch=21, bg="gray70",cex=1.4)
axis(1,at=c(1.76,1.78,1.80,1.82,1.84), lwd=1)
axis(2,at=c(0,0.25,0.5,0.75,1),lwd=1)
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="black",cex=1.4)
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="black",cex=1.4)
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
qRT PCR
C12 T2.5, 3.5, & 4.5
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected", xlim=c(1.7, 1.83),
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Corrected, MC1_T4.5$qPCR_RMAX,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5", "MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley", xlim=c(1.73, 1.85),
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Buckley, MC1_T4.5$qPCR_RMAX,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T3.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected", xlim=c(1.7, 1.83),ylim=c(0,20),
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Corrected, MC1_T4.5$qPCR_conc,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5", "MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley", xlim=c(1.73, 1.85),
ylim=c(0,20),
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Buckley, MC1_T4.5$qPCR_conc,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T3.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
}
#### T2.5
MC1-C12 vs. MC2-Met
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Corrected, MC2_T2.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Buckley, MC2_T2.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0.00001,20))
lines(MC2_T2.5$Corrected, MC2_T2.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0.00001,20))
lines(MC2_T2.5$Buckley, MC2_T2.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
MC1-C12 vs. MC3-Eth
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Corrected, MC3_T2.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Buckley, MC3_T2.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,25))
lines(MC3_T2.5$Corrected, MC3_T2.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,25))
lines(MC3_T2.5$Buckley, MC3_T2.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
}
MC1-C12 vs. MC4-Ace
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Corrected, MC4_T2.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Buckley, MC4_T2.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Corrected, MC4_T2.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Buckley, MC4_T2.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
}
MC1 vs. MC5 - Redo Spin
REDO SPIN
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC5_T2.5$Corrected, MC5_T2.5$qPCR_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC5_T2.5$Buckley, MC5_T2.5$qPCR_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,7.25))
lines(MC5_T2.5$Corrected, MC5_T2.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,7.25))
lines(MC5_T2.5$Buckley, MC5_T2.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
}
MC1 vs. MC6 - Redo Spin
REDO SPIN
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC6_T2.5$Corrected, MC6_T2.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC6_T2.5$Buckley, MC6_T2.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0, 40))
lines(MC6_T2.5$Corrected, MC6_T2.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0, 40))
lines(MC6_T2.5$Buckley, MC6_T2.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
}
T3.5 - redo C12 qRT PCR
MC1-C12 vs. MC2-Met -Redo qRT PCR
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_1Sept22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T3.5$Corrected, MC2_T3.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T3.5$Buckley, MC2_T3.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,20))
lines(MC2_T3.5$Corrected, MC2_T3.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,20))
lines(MC2_T3.5$Buckley, MC2_T3.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
MC1 vs. MC3 - Redo Spin
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC3_T3.5$Corrected, MC3_T3.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC3_T3.5$Buckley, MC3_T3.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0,20))
lines(MC3_T3.5$Corrected, MC3_T3.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0,20))
lines(MC3_T3.5$Buckley, MC3_T3.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
}
MC1-C12 vs. MC4-Ace
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC4_T3.5$Corrected, MC4_T3.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC4_T3.5$Buckley, MC4_T3.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC4_T3.5$Corrected, MC4_T3.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC4_T3.5$Buckley, MC4_T3.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
}
MC1-C12 vs. MC5-Glu - Redo qRT PCR
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC5_T3.5$Corrected, MC5_T3.5$qPCR_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC5_T3.5$Buckley, MC5_T3.5$qPCR_RMAX,type="o", pch=22, bg="#af953c", col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC5_T3.5$Corrected, MC5_T3.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC5_T3.5$Buckley, MC5_T3.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
}
MC1-C12 vs. MC6-Xyl - redo qRT PCR
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Corrected, MC6_T3.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Buckley, MC6_T3.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Corrected, MC6_T3.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Buckley, MC6_T3.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
}
T4.5
MC1-C12 vs. MC2-Met - redo qRT PCR
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T4.5$Corrected, MC1_T4.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T4.5$Corrected, MC2_T4.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T4.5$Buckley, MC2_T4.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,10))
lines(MC2_T4.5$Corrected, MC2_T4.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,10))
lines(MC2_T4.5$Buckley, MC2_T4.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
16S Community Data
library(phyloseq)
x<-read.csv(file='/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/asv-table.csv',header=TRUE,row.names=1)
OTU = otu_table(x, taxa_are_rows=T)
taxa<-read.csv(file="/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/taxonomy.csv",header=TRUE,row.names=1)
t<-as.matrix(taxa)
tax2<-tax_table(t)
map<-import_qiime_sample_data("/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/map_exp4.txt")
tree=read.tree('/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/tree.nwk')
phyo = phyloseq(OTU, tax2,map,tree)
phyo## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 2102 taxa and 96 samples ]
## sample_data() Sample Data: [ 96 samples by 8 sample variables ]
## tax_table() Taxonomy Table: [ 2102 taxa by 8 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 2102 tips and 2100 internal nodes ]phyo1 = subset_taxa(phyo, !Order=="Chloroplast")
phyo2 = subset_taxa(phyo1, !Family=="Mitochondria")
phyo=phyo2
phyo## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1921 taxa and 96 samples ]
## sample_data() Sample Data: [ 96 samples by 8 sample variables ]
## tax_table() Taxonomy Table: [ 1921 taxa by 8 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1921 tips and 1919 internal nodes ]Alpha Diversity
ASV Barplot
phyo_abund=transform_sample_counts(phyo, function(x) (x/sum(x)))
pd <- psmelt(phyo_abund)
colors=readRDS('/Users/oliviaahern/Documents/GitHub/Exp4/colors_asvs.rds')
library(grid)
#palette(as.character(t(colors)))
d_rgn = ggplot(pd, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = Strain)) +
scale_fill_manual(values=as.character(t(colors))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~Treatment, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "ASV Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "none",
panel.grid=element_blank(),
strip.text.x = element_text(
size = 10, color = "black", face = "bold"),
strip.background = element_rect(
color="white", fill="white", size=1, linetype="solid"),
panel.spacing = unit(0.05, "lines"))
d_rgn
interactive ASV Barplot > 0.001%
Under construction
phyo_nop=subset_samples(phyo, B_C!='pond')
library(plyr)
# get abundance in %
phy <- transform_sample_counts(phyo_nop, function(x) x/sum(x))
# create dataframe from phyloseq object
dat <- psmelt(phy)
# convert Phylum to a character vector from a factor because R
dat$OTU <- as.character(dat$OTU)
# group dataframe by Phylum, calculate median rel. abundance
medians <- ddply(dat, ~OTU, function(x) c(median=median(x$Abundance)))
# find Phyla whose rel. abund. is less than 0.1%
remainder <- medians[medians$median <= 0.00001,]$OTU
# change their name to "Other"
dat[dat$OTU %in% remainder,]$OTU <- 'Other <0.1%'
# boxplot
blah=data.frame(tax_table(phyo_abund))
nan=cbind(row.names(blah), (colors))
nano = data.frame(nan)
colnames(nano) = c("OTU", "Colors")
subs=levels(as.factor(dat$OTU))
sub=subset(nano, OTU %in% subs)
color2=c(sub$Colors, 'gray80')
p_rgn = ggplot(dat, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = OTU)) +
scale_fill_manual(values=as.character(t((color2)))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "ASV Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "bottom",
panel.grid=element_blank(),
legend.text = element_text(size=6),
legend.key.size = unit(0.25,'cm'),
#strip.text.x = element_text(
# size = 10, color = "black", face = "bold"),
#strip.background = element_rect(
# color="white", fill="white", size=1, linetype="solid"),
#panel.spacing = unit(0.05, "lines")
)
p_rgn
#library(plotly)
#fig <- ggplotly(p_rgn)
#figinteractive Genera Barplot
Working on this plot
phyo_nop_g=tax_glom(phyo_nop, taxrank="Genus")
library(plyr)
# get abundance in %
phy <- transform_sample_counts(phyo_nop_g, function(x) x/sum(x))
# create dataframe from phyloseq object
dat <- psmelt(phy)
# convert Phylum to a character vector from a factor because R
dat$Genus <- as.character(dat$Genus)
dat$Genus[dat$Genus==""] <- NA
# group dataframe by Phylum, calculate median rel. abundance
medians <- ddply(dat, ~Genus, function(x) c(median=median(x$Abundance)))
# find Phyla whose rel. abund. is less than 0.1%
remainder <- medians[medians$median <= 0.00001,]$Genus
# change their name to "Other"
dat[dat$Genus %in% remainder,]$Genus <- 'Other <0.1%'
# boxplot
blah=data.frame(tax_table(phyo_abund))
nan=cbind(blah$Genus, (colors))
nano = data.frame(nan)
colnames(nano) = c("Genus", "Colors")
subs=levels(as.factor(dat$Genus))
sub=subset(nano, Genus %in% subs)
color4=c(sub$Colors, 'gray80')
p_rgn = ggplot(dat, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = Genus)) +
scale_fill_manual(values=as.character(t((color4)))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "Genus Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "bottom",
panel.grid=element_blank(),
legend.text = element_text(size=6),
legend.key.size = unit(0.25, 'cm')
#strip.text.x = element_text(
# size = 10, color = "black", face = "bold"),
#strip.background = element_rect(
# color="white", fill="white", size=1, linetype="solid"),
#panel.spacing = unit(0.05, "lines")
)
p_rgn
#library(plotly)
#fig <- ggplotly(p_rgn)
#figClass Barplot
micro=microbiome::aggregate_taxa(phyo, "Class")
phyo_abund=transform_sample_counts(micro, function(x) (x/sum(x)))
pd <- psmelt(phyo_abund)
colors=readRDS("/Users/oliviaahern/Documents/GitHub/Exp4/c_class.rds")
library(grid)
#palette(as.character(t(colors)))
d_rgn = ggplot(pd, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = Class)) +
scale_fill_manual(values=as.character(t(colors))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "Class Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "bottom",
panel.grid=element_blank(),
strip.text.x = element_text(
size = 10, color = "black", face = "bold"),
legend.text = element_text(size=6),
legend.key.size = unit(0.25, 'cm')
#strip.background = element_rect(
# color="white", fill="white", size=1, linetype="solid"),
# panel.spacing = unit(0.05, "lines"))
)
d_rgn
Beta Diversity
Aitchison’s Distance
Euclidean distance of centered log ratio transformed data
PCoA with Pond
Transform data - remove ASVs that are less than 0.01% of total dataset and minimum reads of 2. Aitchinson’s distance - Euclidean distance of centered log ratio data.
library(CoDaSeq)
library(compositions)
input=t(data.frame(otu_table(phyo)))
dim(input)## [1] 96 1921d.subset <- codaSeq.filter(input,
samples.by.row=T,min.reads=2,min.prop =0.0001)
dim(d.subset)## [1] 1145 96log_rats <- (compositions::clr(t(d.subset)))
OTU=otu_table(t(log_rats),taxa_are_rows = T)
comp_clr=phyloseq(OTU,map,tax2)
otu=t(otu_table(comp_clr))
euc=vegdist(otu,'euc')
p=prcomp(euc)
# summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(comp_clr)$pch,
bg=sample_data(comp_clr)$col,cex.lab=1.3,
xlab= 'PCoA1 62.10%', ylab='PCoA2 13.71%',cex=1.5)
legend(60,60, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat",
"Pond"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f",
"black"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23, 24),
bty='n',cex=1)
ordiellipse(p, groups=sample_data(comp_clr)$Timepoint)
}
PCoA no Pond
Transform data - remove ASVs that are less than 0.01% of total dataset and minimum reads of 2. Aitchinson’s distance - Euclidean distance of centered log ratio data.
data1=subset_samples(phyo, Treatment !="Pond")
input=t(data.frame(otu_table(data1)))
dim(input)## [1] 94 1921d.subset <- codaSeq.filter(input,
samples.by.row=T,min.reads=2,min.prop =0.0001)
dim(d.subset)## [1] 748 94log_rats <- (compositions::clr(t(d.subset)))
OTU=otu_table(t(log_rats),taxa_are_rows = T)
comp_clr=phyloseq(OTU,map,tax2)
otu=t(otu_table(comp_clr))
euc=vegdist(otu,'euc')
p=prcomp(otu)
#summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 29.17%', ylab='PCoA2 11.24%',cex=1.5)
legend(12,20, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23),
bty='n',cex=1)
ordiellipse(p, groups=sample_data(comp_clr)$Timepoint)
}
Batch PCoA
Ellipses represent 80% confidence intervals around the centroid of the Timepoint.
Data is significantly tied to the timepoint sampled (adonis2, R2=0.23, F=9.4, p<0.001) not the Treatment/MC (adonis2, R2=0.08, F=0.7, p=0.973).
data1=subset_samples(comp_clr, B_C =="Batch")
otu=t(otu_table(data1))
euc=vegdist(otu,'euc')
p=prcomp(otu)
#summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 31.54%', ylab='PCoA2 14.79%',cex=1.5)
ordiellipse(p, groups=sample_data(data1)$Timepoint,
label=FALSE)
legend(12,5, legend=c("MC1-C12 Batch",
"MC2-Met Batch",
"MC3-Eth Batch",
"MC4-Ace Batch",
"MC5-Glu Batch",
"MC6-Xyl Batch"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=21,
bty='n',cex=1)
}
adonis2(euc~sample_data(data1)$Timepoint + sample_data(data1)$Treatment,
by='margin')## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = euc ~ sample_data(data1)$Timepoint + sample_data(data1)$Treatment, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(data1)$Timepoint 1 2581.6 0.22551 9.3967 0.001 ***
## sample_data(data1)$Treatment 5 899.0 0.07853 0.6544 0.974
## Residual 29 7967.4 0.69596
## Total 35 11448.0 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Chemostat PCoA
Ellipses represent 80% confidence intervals around the centroid of the Treatment.
Chemostat data is significantly associated with both Timepoint (adonis2, R2=0.06, F=5.5, p<0.001) and Treatment/MC (adonis2, R2=0.39, F=6.8, p<0.001).
data1=subset_samples(comp_clr, B_C =="Chemostat")
otu=t(otu_table(data1))
euc=vegdist(otu,'euc')
p=prcomp(otu)
#summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 17.66%', ylab='PCoA2 12.52%',cex=1.5)
ordiellipse(p, groups=sample_data(data1)$Treatment,label=TRUE)
legend(15.5,5, legend=c("MC1-C12 Chemostat",
"MC2-Met Chemostat",
"MC3-Eth Chemostat",
"MC4-Ace Chemostat",
"MC5-Glu Chemostat",
"MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=23,
bty='n',cex=1)
}
adonis2(euc~sample_data(data1)$Timepoint + sample_data(data1)$Treatment,
by='margin')## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = euc ~ sample_data(data1)$Timepoint + sample_data(data1)$Treatment, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(data1)$Timepoint 1 679.1 0.06347 5.5055 0.001 ***
## sample_data(data1)$Treatment 5 4222.4 0.39465 6.8461 0.001 ***
## Residual 47 5797.5 0.54187
## Total 53 10699.0 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Phylogenetic Distance (philr)
PCoA with Pond
library(philr)
GP <- transform_sample_counts(phyo, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')## [1] "Species_/Kingdom_Bacteria"otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(phyo)$pch,
bg=sample_data(phyo)$col,cex.lab=1.3,
xlab= 'PCoA1 79.27%', ylab='PCoA2 9.19%',cex=1.5)
legend(80,45, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat",
"Pond"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f",
"black"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23, 24),
bty='n',cex=1)
}
PCoA no Pond
Samples significantly tied to
- Treatment (aka MC) R2 = 0.16, F = 6.26, p < 0.001
- Timepoint R2 = 0.021, F = 5.33, p = 0.007
- Batch or Chemostat R2 = 0.05, F=12.80, p < 0.001
phyo1=subset_samples(phyo, B_C !="Pond")
GP <- transform_sample_counts(phyo1, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')## [1] "Species_/Kingdom_Bacteria"otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(phyo1)$pch,
bg=sample_data(phyo1)$col,cex.lab=1.3,
xlab= 'PCoA1 78.84%', ylab='PCoA2 9.93%',cex=1.5)
legend(80,45, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23),
bty='n',cex=1)
}
adonis2(gp.dist~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint + sample_data(phyo1)$B_C, by='margin')## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = gp.dist ~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint + sample_data(phyo1)$B_C, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(phyo1)$Treatment 5 2060.8 0.12580 6.2597 0.001 ***
## sample_data(phyo1)$Timepoint 1 351.2 0.02144 5.3335 0.003 **
## sample_data(phyo1)$B_C 1 842.8 0.05145 12.7998 0.001 ***
## Residual 82 5399.1 0.32959
## Total 89 16381.4 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Batch PCoA
Samples significantly tied to
- Treatment (aka MC) R2 = 0.04, F = 0.3267, p = 0.99
- Timepoint R2 = 0.21501, F = 8.3907, p = 0.002
phyo1=subset_samples(phyo, B_C =="Batch")
GP <- transform_sample_counts(phyo1, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')## [1] "Species_/Kingdom_Bacteria"otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(phyo1)$pch,
bg=sample_data(phyo1)$col,cex.lab=1.3,
xlab= 'PCoA1 64.96%', ylab='PCoA2 18.17%',cex=1.5)
ordiellipse(p, groups=sample_data(phyo1)$Timepoint,
label=TRUE, cex=1.5)
legend(90,20, legend=c("MC1-C12 Batch",
"MC2-Met Batch",
"MC3-Eth Batch",
"MC4-Ace Batch",
"MC5-Glu Batch",
"MC6-Xyl Batch"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=21,
bty='n',cex=1)
}
adonis2(gp.dist~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by='margin')## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = gp.dist ~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(phyo1)$Treatment 5 818.1 0.04186 0.3267 0.989
## sample_data(phyo1)$Timepoint 1 4202.7 0.21501 8.3907 0.003 **
## Residual 29 14525.5 0.74313
## Total 35 19546.3 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Chemostat PCoA
Samples significantly tied to
- Treatment (aka MC) R2 = 0.58701, F = 16.814, p = 0.001
- Timepoint R2 = 0.08482, F = 12.148, p = 0.001
phyo1=subset_samples(phyo, B_C =="Chemostat")
GP <- transform_sample_counts(phyo1, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')## [1] "Species_/Kingdom_Bacteria"otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 53.93%', ylab='PCoA2 24.54%',cex=1.5)
ordiellipse(p, groups=sample_data(data1)$Treatment,label=TRUE)
legend(85,50, legend=c("MC1-C12 Chemostat",
"MC2-Met Chemostat",
"MC3-Eth Chemostat",
"MC4-Ace Chemostat",
"MC5-Glu Chemostat",
"MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=23,
bty='n',cex=1)
}
adonis2(gp.dist~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by='margin')## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = gp.dist ~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(phyo1)$Treatment 5 12134.8 0.58701 16.814 0.001 ***
## sample_data(phyo1)$Timepoint 1 1753.5 0.08482 12.148 0.001 ***
## Residual 47 6784.0 0.32817
## Total 53 20672.3 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1